Hello, I am looking for an application that will map paired-end reads and form a consensus sequence. I believe pandaseq can do this, but would appreciate if anyone has another recommendation.
Thanks
Thanks
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are you referring to slop-tigs where paired-end sequence was done to a fragment that is smaller than 2*read_length ?
Check out FLASH. -
slop-tigs, nice.. actually amplicons where yes, the 2X read-length is greater than the amplicon length.
Thanks, I'll look for FLASHComment
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This is the full list of bioinformatics software. You should be able to text-search for 'paired' and come up with some. http://seqanswers.com/wiki/Software/list
SHRiMP (http://compbio.cs.toronto.edu/shrimp/) and bowtie (http://bowtie-bio.sourceforge.net/index.shtml) produce SAM/BAM output which can then be used with a plethora of software suites which can produce a consensus. Samtools (http://samtools.sourceforge.net/), GATK (http://www.broadinstitute.org/gsa/wi...alysis_Toolkit), and Picard tools (http://picard.sourceforge.net/comman...overview.shtml) are some that can analyze these files and report your consensus sequence.
I hope this helps!Comment
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